Hi Beth
I'm not sure what the answer is. Did you prune back to just above a leaf node?. Normally if you do this the plant will not rot further down the stem. If you pruned to just below a leaf joint, the plant may die back to the next node. I have read, but not tried, that if you treat the cut surface of the stem with Isopropyl alcohol, this will help prevent rot.
Hope this helps
Ron